Leaders of the two countries, meeting for a summit in Spain on Tuesday, agreed to start inspecting vessels deemed dangerous, and if appropriate, to force them out of the 320-kilometre (200 mile) economic exclusion zone around their coastlines.
It means all single-hulled vessels over 15 years old will be subject to exhaustive checks.
"We have decided that as of tomorrow (Wednesday) all the vessels of a dubious character will be liable to be inspected and, if need be, excluded from our 200-mile zones," said French President Jacques Chirac.
Single-hulled tankers like the Prestige are likely to be particularly targeted by the maritime patrols.
Spanish Prime Minister Jose Maria Aznar confirmed at a press conference that the two countries had agreed to push ahead with the measures without waiting for the rest of the European Union to endorse the plan.
The Prestige shed an estimated 11,000 metric tons of its cargo of around 70,000 tons of fuel oil, polluting miles of the Galician coastline, killing seabirds and halting fishing.
The rest of the cargo went down with the ship, where authorities hope it will solidify.
Volunteers cleaning
Maritime safety emerged as the top priority of the summit, held in the southern city of Malaga.
The proposals will now be put to next month's European summit in Copenhagen, inviting other members to also adopt them, said Mr Chirac.
Hundreds of volunteers have joined the effort to scrape oil from up to 400 Spanish beaches.
Two special pumping ships have been used to remove up to 2,000 tons still at sea.